Project Summary/Abstract Humans coexist with trillions of microorganisms living amongst them. We as a species have never existed without them. Thus, these complex communities of microbes that include bacteria, fungi, protozoa, and viruses play a fundamental role in controlling all aspects of our physiology. The last 20 years of research has focused almost exclusively on our symbiotic bacteria. This work has revealed the important contribution of alterations in the composition of our gut bacteria to many immune disorders, but especially inflammatory bowel disease (IBD). Furthermore, these large-scale efforts have resulted in tangible and emerging new therapies for IBD that include fecal transplantation and controlled antibiotic use. The discoveries will also enable us to start stratifying different IBD patients by their genetics and resident bacteria for precision therapy. New technologies only in last couple of years such as large-scale sequencing or ?metagenomics? have allowed us to identify and appreciate the important contribution of viruses to the microbial communities that inhabit the healthy intestine, i.e. ?the virome?. Moreover, a recent analysis of stool from IBD patients found that the virome was indeed significantly altered. In mice, a protective function of intestinal viruses in the gut has been demonstrated. How the virome contributes to host immune responses that enable a healthy gut or how changes in virus composition impacts gut inflammation is almost completely unknown. This is both daunting and exciting. Learning from the microbiome field, at this juncture in virome research, it is essential that we move beyond correlations and toward a detailed mechanistic understanding of how certain viruses educate our immune system for health and disease. Here we propose to distinguish the dominant components of the intestinal virome that shape our immune system in the gut. We propose to understand the interaction of the human intestinal virome with viral sensors of the immune system using crosslinking immunoprecipitation (CLIP). Mammalian cells are endowed with the ability to detect viral nucleic acids through several pattern recognition receptors, such as RNA sensors RIG-I or MDA-5. We will directly examine the composition of the RNA virome that is immunoprecipitated with RIG-I or MDA-5 in human intestinal tissue. We will then characterize the precise immune responses that the identified viral RNAs trigger in health and if this is lost and/or replaced by other viruses in IBD. Thus, this work will for the first time identify the virus members that the host immune system sees and responds to in health and disease. Moreover, it will provide the first evidence of how viruses can help build gut immunity in humans - a contrast to the misconception that all viruses are harmful. The ability to identify these immunomodulatory commensal viruses will also represent a first step towards developing personalized, virome-focused therapies that may reduce, reverse or even prevent IBD development through targeted elimination or replacement of disease- or health-driving intestinal viruses, respectively.